Gene expression analysis is becoming more common now that sequence information for DNA is readily available. One way of obtaining information about genes involves the use of an array of probes. One type of probe is made on a silicon array of cells, consisting of DNA fragments or oligomers attached at each cell. The DNA probe is used to hybridize marked RNA transcripts, or more typically their cDNA counterparts, produced by a target gene. The DNA probe in the array is exposed to the RNA transcripts or cDNAs, which then attach or hybridize to the DNA probes if they match. Unattached RNAs or cDNAs are washed away, and the array is exposed to laser light causing the attached RNA associated fluorophores to fluoresce. The amount of fluorescence is measured and is representative of the expression level of the gene.
Millions of independent gene expression measurements are made each year using different probes. There are serious obstacles to accurately mining and systematically integrating the measurements. Since probes exhibit different sensitivities, it is difficult to compare results from different probes. Several problems are encountered, including how to compare expression levels between different genes, how to determine absolute expression values, and how to eliminate cross-hybridization signals. The present invention provides a means to overcome these difficulties.